MaxQB - The MaxQuant DataBase
and displays collections of large proteomics projects
and allows joint analysis and comparison. As a first dataset is contains proteome data
of 11 different human cell lines. The 11 cell line proteomes together
identify proteins expressed from more than half of all
human genes. For each protein of interest, expression
levels estimated by label-free quantification can be visualized
across the cell lines. Similarly, the expression
rank order and estimated amount of each protein within
each proteome are plotted. MaxQB is described in more detail in the accompanying
Christoph Schaab, Tamar Geiger, Gabriele Stoehr, Juergen Cox and Matthias Mann:
"Analysis of high-accuracy, quantitative proteomics data in the MaxQB database",
Mol Cell Proteomics 11 (2012) M111.014068.
New Data Sets
- Minimalistic Sample Processing:
The in-StageTip sample preparation method largely
eliminates contamination or losses and is extremely robust and
scalable. Peptides can be eluted in several fractions or in one step
for single-run proteomics. In one day of gradient time we obtained
the largest proteomes for budding and fission yeast to date and found
that their protein copy numbers correlated highly (R2 = 0.78).
Applying the in-StageTip method to quadruplicate measurements of a
human cell line yielded copy number estimates for 9,667 human
proteins and demonstrated excellent quantitative reproducibility
between replicates (R2 = 0.97).
Go to project
- Quantitative Proteomic Map of Mouse Tissues:
proteomic analysis of twenty-eight mouse tissues using high-resolution mass
spectrometry and used a mix of SILAC mouse tissues as a spike-in internal
standard for accurate protein quantification across these tissues. We identified a
total of 7,349 proteins and quantified 6,974 of them. Bioinformatic data analysis
showed that physiologically related tissues cluster together and that highly
expressed proteins represent the characteristic tissue functions. Tissue
specialization is reflected prominently in the proteomic profiles and is apparent
already in their hundred most abundant proteins. The proportion of strictly tissue
specific proteins appears to be small. However, even proteins with household
function, such as those in ribosomes and spliceosomes, can have dramatic
expression differences between tissues.
Go to project
- TRAIL induced Apoptosis:
We detect caspase-dependent cleavage substrates by quantifying
protein intensities before and after TRAIL induction in SDS gel
slices. Apoptotic protein cleavage events are identified by a
characteristic SILAC ratio pattern across gel slices that results from
differential migration of the cleaved versus the uncleaved protein.
Our approach identified more than 650 of these cleaved
proteins in response to TRAIL-induced apoptosis, including many
previously unknown substrates and cleavage sites.
Go to project